Add x,y coordinates of stereographic projection of given direction (pole) in crystal frame.

This commit is contained in:
Philip Eisenlohr 2014-12-13 00:12:55 +00:00
parent 05d7adaf25
commit 89f8ba979e
1 changed files with 166 additions and 0 deletions

166
processing/post/addPole.py Executable file
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#!/usr/bin/env python
# -*- coding: UTF-8 no BOM -*-
import os,sys,string
import numpy as np
from optparse import OptionParser
import damask
scriptID = string.replace('$Id$','\n','\\n')
scriptName = os.path.splitext(scriptID.split()[1])[0]
# --------------------------------------------------------------------
# MAIN
# --------------------------------------------------------------------
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
Add x,y coordinates of stereographic projection of given direction (pole) in crystal frame.
""", version = scriptID)
parser.add_option('-p', '--pole', dest='pole', type='float', nargs=3, metavar='float float float',
help = 'crystal frame direction for pole figure %default')
parser.add_option('--polar', dest='polar', action='store_true',
help = 'output polar coordinates r,phi [%default]')
parser.add_option('-e', '--eulers', dest='eulers', metavar='string',
help = 'Euler angles label')
parser.add_option('-d', '--degrees', dest='degrees', action='store_true',
help = 'Euler angles are given in degrees [%default]')
parser.add_option('-m', '--matrix', dest='matrix', metavar='string',
help = 'orientation matrix label')
parser.add_option('-a', dest='a', metavar='string',
help = 'crystal frame a vector label')
parser.add_option('-b', dest='b', metavar='string',
help = 'crystal frame b vector label')
parser.add_option('-c', dest='c', metavar='string',
help = 'crystal frame c vector label')
parser.add_option('-q', '--quaternion', dest='quaternion', metavar='string',
help = 'quaternion label')
parser.set_defaults(pole = [1.0,0.0,0.0])
parser.set_defaults(degrees = False)
parser.set_defaults(polar = False)
(options, filenames) = parser.parse_args()
datainfo = { # list of requested labels per datatype
'tensor': {'len':9,
'label':[]},
'vector': {'len':3,
'label':[]},
'quaternion': {'len':4,
'label':[]},
}
input = []
if options.eulers != None:
datainfo['vector']['label'] += [options.eulers]
input += ['eulers']
if options.a != None and \
options.b != None and \
options.c != None:
datainfo['vector']['label'] += [options.a,options.b,options.c]
input += ['frame']
if options.matrix != None:
datainfo['tensor']['label'] += [options.matrix]
input += ['matrix']
if options.quaternion != None:
datainfo['quaternion']['label'] += [options.quaternion]
input += ['quaternion']
if len(input) != 1: parser.error('needs exactly one input format...')
input = input[0]
toRadians = np.pi/180.0 if options.degrees else 1.0 # rescale degrees to radians
pole = np.array(options.pole)
pole /= np.linalg.norm(pole)
#--- setup file handles --------------------------------------------------------------------------
files = []
if filenames == []:
files.append({'name':'STDIN',
'input':sys.stdin,
'output':sys.stdout,
'croak':sys.stderr,
})
else:
for name in filenames:
if os.path.exists(name):
files.append({'name':name,
'croak':sys.stdout,
})
#--- loop over input files ------------------------------------------------------------------------
for file in files:
if file['name'] != 'STDIN':
file['input'] = open(file['name'])
file['output'] = open(file['name']+'_tmp','w')
file['croak'].write('\033[1m' + scriptName + '\033[0m' + (': '+file['name'] if file['name'] != 'STDIN' else '') + '\n')
table = damask.ASCIItable(file['input'],file['output'],buffered = False) # make unbuffered ASCII_table
table.head_read() # read ASCII header info
table.info_append(scriptID + '\t' + ' '.join(sys.argv[1:]))
column = {}
missingColumns = False
for datatype,info in datainfo.items():
for label in info['label']:
key = list(set([label, '1_'+label]) & set(table.labels))
if key == []:
file['croak'].write('column %s not found...\n'%label)
missingColumns = True # break if label not found
else:
column[label] = table.labels.index(key[0]) # remember columns of requested data
if missingColumns:
continue
# ------------------------------------------ assemble header ---------------------------------------
table.labels_append(['%i_pole_%g%g%g'%(i+1,options.pole[0],options.pole[1],options.pole[2]) for i in xrange(2)])
table.head_write()
# ------------------------------------------ process data ------------------------------------------
outputAlive = True
while outputAlive and table.data_read(): # read next data line of ASCII table
if input == 'eulers':
o = damask.Orientation(Eulers=toRadians*\
np.array(map(float,table.data[column[options.eulers]:\
column[options.eulers]+datainfo['vector']['len']])),
)
elif input == 'matrix':
o = damask.Orientation(matrix=\
np.array([map(float,table.data[column[options.matrix]:\
column[options.matrix]+datainfo['tensor']['len']])]).reshape(np.sqrt(datainfo['tensor']['len']),
np.sqrt(datainfo['tensor']['len'])).transpose(),
)
elif input == 'frame':
o = damask.Orientation(matrix=\
np.array([map(float,table.data[column[options.a]:\
column[options.a]+datainfo['vector']['len']] + \
table.data[column[options.b]:\
column[options.b]+datainfo['vector']['len']] + \
table.data[column[options.c]:\
column[options.c]+datainfo['vector']['len']]
)]).reshape(3,3),
)
elif input == 'quaternion':
o = damask.Orientation(quaternion=\
np.array(map(float,table.data[column[options.quaternion]:\
column[options.quaternion]+datainfo['quaternion']['len']])),
)
rotatedPole = o.quaternion*pole # rotate pole according to crystal orientation
(x,y) = rotatedPole[0:2]/(1.+abs(pole[2])) # stereographic projection
table.data_append([np.sqrt(x*x+y*y),np.arctan2(y,x)] if options.polar else [x,y]) # cartesian coordinates
outputAlive = table.data_write() # output processed line
# ------------------------------------------ output result -----------------------------------------
outputAlive and table.output_flush() # just in case of buffered ASCII table
table.input_close() # close input ASCII table (works for stdin)
table.output_close() # close output ASCII table (works for stdout)
if file['name'] != 'STDIN':
os.rename(file['name']+'_tmp',file['name']) # overwrite old one with tmp new